The field experiment was carried out in three cotton growing seasons from 2011 to 2013. Cotton canopy normalized difference vegetation index (NDVI) was obtained by GreenSeeker at full bud stage, flowering stage, full boll stage, early wadding stage. Yields, from different nitrogen application rates, were collected at harvest stage and compared with each other. Canopy NDVI, changing with nitrogen application level and growth period, were analyzed, separately. Furthermore, the correlation analysis was done between yield and canopy NDVI. Yield estimation models were established for cotton based on NDVI value. Results indicate that, in the four growth stages, with N rates increasing, canopy NDVI value presents a trend of “low high low”. And the correlation coefficient between canopy NDVI and yield is 0.7137，0.8479，0.8979，0.6926, respectively, and significantly positive correlative at flowering stage(P=0.0034) as well as full boll stage (P=0.0008). Regression between predicted yield and measured yield values of the year of 2013 shows that the correlation coefficient is maximum at full boll stage (R2=0.9082), and the root mean square error(RMSE) is 301.67kg/hm2, while the relative error (5.15%) is minimum. The results suggest that it is especially feasible to use canopy NDVI to estimate yield of cotton at the full boll stage.